Hiv-1 incidence biomarkers

Abstract

The invention is directed to methods, reagents and kits for detecting incident HIV-1 infection.

What is claimed is: 
     
         1 . A method for classifying HIV-1 status of a sample from a subject as recent or long standing, the method comprising:
 a) Measuring in the sample binding of IgG3 antibodies to Clade C gp140 envelope (measurement X1);   b) Measuring in the sample the avidity of IgG4 antibodies binding to T/F Clade C gp140 envelope (measurement X2);   c) Measuring in the sample the avidity of IgG4 antibodies binding to Clade B gp140 envelope (measurement X3);   d) Measuring in the sample the avidity of IgG to gp41 immunodomninant domain (ID) epitope (measurement X4), wherein the avidity of IgG gp41 ID epitope is determined as difference between IgG Citrate gp41 ID epitope and IgG PBS gp41 ID epitope;   e) Using measurements X1, X2, X3 and X4 to determine recent (R) or longstanding (L) discriminant value (DV j  is used interchangeably C j ), wherein “j” is recent (R) or longstanding (L) class, wherein cut off period for R is nine months, and wherein
 i. DV R =co R +C 1R X1+c 2R X2+c 3R X3+c 4R X4, wherein R classification coefficients are as follows: Table 40 or Table 41, and 
 ii. DV L =co L +c 1L X1+c 2L X2+c 3L X3+c 4L X4, wherein L classification coefficients are as follows: Table 40 or Table 41; and 
   f) Classifying a sample as being a recent infection or a long-standing infection, wherein if DV R  is larger than DV L , the sample is classified as Recent, or wherein if DV L  is larger than DV R , the sample is classified as Longstanding.   
     
     
         2 . The method of  claim 1 , wherein Clade C gp140 envelope for measurement X1 is any one Clade C envelope in  FIG. 62 . 
     
     
         3 . The method of  claim 2 , wherein Clade C gp140 envelope for measurement X1 is BF1266 gp140 ( FIG. 59 ), comprising LANL database accessioning number HM215360. 
     
     
         4 . The method of  claim 1 , wherein T/F Clade C gp140 envelope for measurement X2 is any one of the T/F clade C envelopes in  FIG. 62 . 
     
     
         5 . The method of  claim 4 , wherein the T/F clade C gp140 for measurement X2 is T/F CH505 gp140 ( FIG. 59 ), comprising LANL database accessioning number KC247557. 
     
     
         6 . The method of  claim 1 , wherein the clade B gp140 envelope for measurement X3 is any one of Clade B envelopes in  FIG. 62 , comprising LANL database accessioning number AY835447, AY835441, or AY835451. 
     
     
         7 . The method of  claim 6 , wherein the clade B gp140 envelope for measurement X3 is SC42261 gp140 in  FIG. 59 , comprising LANL database accessioning number AY835441. 
     
     
         8 . The method of  claim 1 , wherein the gp41 ID epitope for measurement X4 is any one listed in  FIG. 62 . 
     
     
         9 . The method of  claim 8 , wherein the gp41 ID epitope for measurement X4 is B.con03 B.con03 ID/(Bio-GGG-BC.con03 ID), comprising amino acid sequence: Bio-GGG-KQLQARVLAVERYLKDQQLLGIWGCSGKLICTTAV. 
     
     
         10 . The method of  claim 1 , wherein the Clade C gp140 envelope for measurement X1 is BF1266 gp140 ( FIG. 59 ), the T/C clade C gp140 for measurement X2 is T/F CH505 gp140 ( FIG. 59 ), the clade B gp140 envelope for measurement X3 is SC42261 gp140 ( FIG. 59 ) and the gp41 ID epitope for measurement X4 is B.con03 ID/(Bio-GGG-BC.con03 ID). 
     
     
         11 . The method of  claim 1  or  10 , wherein
 i. For DV R =co R +c 1R X1+c 2R X2+c 3R X3+c 4R X4, the R classification coefficients are as follows: Table 40, and 
 ii. For DV L =co L +c 1L X1+c 2L X2+c 3L X3+c 4L X4, the L classification coefficients are as follows: Table 40; and 
 iii. wherein if DV R  is larger than DV L , the sample is classified as Recent, or wherein if DV L  is larger than DV R  the sample is classified as Longstanding. 
 
     
     
         12 . A method for classifying HIV-1 status of a sample from a subject as recent or long standing, the method comprising:
 Detecting and quantifying the formation of antibody-antigen complexes, wherein the antibody-antigen complexes comprise:
 i. avidity of IgG3 antibodies to p66 (measurement p66X1), 
 ii. avidity of IgM antibodies binding to gp41 (measurement gp41X2), 
 iii. avidity of IgG4 antibodies binding to envelope WITO4160 gp140 (measurement WITOX3), 
 iii. binding of IgM to gp41 immunodomninant domain (IG) (measurement gp41X4), 
   Measuring in the sample the avidity of IgG3 antibodies to p66 (measurement p66X1);   Measuring in the sample the avidity of IgM antibodies binding to gp41 (measurement gp41X2);   Measuring in the sample the avidity of IgG4 antibodies binding to envelope WITO4160 gp140 (measurement WITOX3), comprising LANL database accessioning number AY835451;   Measuring in the sample binding of IgM to gp41 (measurement gp41X4); and   Using measurements X1, X2, X3 and X4 to determine recent (R) or longstanding (L) discriminant value (DV j  is used interchangeably C j ), wherein “j” is recent (R) or longstanding (L) class, wherein cut off period for R is nine months, and wherein
 i. DV R =co R +c 1R X1+c 2R X2+c 3R X3+c 4R X4, wherein R classification coefficients are as follows: Table 41, and 
 ii. DV L =co L +c 1L X1+c 2L X2+c 3L X3+c 4L X4, wherein L classification coefficients are as follows: Table 41; and 
   Classifying the HIV status in the sample as being a recent infection or a long-standing infection, wherein if DV R  is larger than DV L , the sample is classified as Recent, or wherein if DV L  is larger than DV R  the sample is classified as Longstanding.   
     
     
         13 . The method of  claim 12 , wherein gp41 comprises Clade B (MN) gp41 protein. 
     
     
         14 . A kit comprising a selection of HIV-1 antigens to determine measurements X1, X2, X3 and X4 of  claims 1 - 12  or the measurements of  claim 13  in a biological sample. 
     
     
         15 . The kit of  claim 14 , wherein the HIV-1 antigens are immobilized on a solid support. 
     
     
         16 . The kit of  claim 14 , wherein the HIV-1 antigens are conjugated to beads. 
     
     
         17 . The kit of  claim 14  further comprising instructions on how to carry out the steps of any one of the above  claim 1 - 12  or  13 . 
     
     
         18 . The kit of  claim 17 , wherein the instructions include instructions on determining DV R  and DV L , and the   
     
     
         19 . The kit of any one of  claims 14 - 18 , wherein the sample is plasma, serum, finger stick blood, dried blood spot (DBS), whole blood, saliva, urine, mucosal fluid, or any other suitable biological sample. 
     
     
         20 . The method of any one of  claims 1 - 13 , wherein the sample is plasma, serum, finger stick blood, dried blood spot (DBS), whole blood, saliva, urine, mucosal fluid, or any other suitable biological sample.